Under the current fare structure, it's not a huge problem. The LD trains running on the NEC are mostly only charging riders to ride to WAS. For MIA-WAS (Star or Meteor), leaving March 9, the fares are $114/$143/$310 (Saver/Value/Flexible); MIA-PHL is $116/$145/$316; MIA-NYP is $118/$147/$320. On the Regionals bracketing the Star's scheduled arrival in WAS on the 10th, WAS-NYP is $49/$88/$173.
Selling the seat from WAS-NYP is a gamble by Amtrak that a MIA-WAS passenger doesn't cancel and that no replacement MIA-WAS passenger can be found (under simplifying assumptions that an available MIA-NYP rider can always be found and that there are no stops between MIA and WAS where a rider can get off the train; if those simplifying assumptions don't hold, then the analysis points even more to "sell the seat" by reducing the risk and/or increasing the reward). As with all gambles, whether the bet should be taken (by selling the WAS-NYP seat) is a question of the risk and reward. The risk is the MIA-NYP fare ($118/$147/$320). The reward is the sum of the MIA-WAS and WAS-NYP fares (if WAS-NYP is at the Regional fares, $163/$231/$483, ignoring such possibilities as Saver MIA-WAS -> Flexible WAS-NYP). As long as the MIA-WAS passenger on Saver cancels 27% or less of the time, Amtrak's expected value is positive*. For Value passengers, Amtrak is still ahead even if they lose the bet 36% of the time, and a 33% cancellation rate among Flexible fares is still break-even for Amtrak. For any loss rate deemed acceptable, a fare for WAS-NYP can be defined which has positive EV for Amtrak (the limiting case would be charging the WAS-NYP rider the fare for MIA-NYP: then even if every MIA-WAS rider cancelled, Amtrak would be no worse for wear!). Amtrak presumably has data on propensity for reservations to be cancelled (if they don't, paying a team of software engineers and statisticians a million bucks a year to get that data may have the single greatest return on investment of anything Amtrak could do right now), which could easily be used to adjust offered fares for LD trains on the NEC.
*: Let's say that of a 100 seats sold on the Star WAS-NYP to fill seats vacated by MIA-WAS passengers, we have 27 MIA-WAS passengers cancel (all 200 reservations were Saver fares). Then Amtrak collects $13,222 in fares. If instead we had 73 MIA-WAS passengers and 27 MIA-NYP passengers booking seats originally taken by MIA-WAS and not sold from WAS-NYP, Amtrak would collect $11,508 in fares.